Download MendeleyCrystal Structure of P450BM3 with decoy molecules
Cong, Z., Shoji, O., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y.To be published.
5B2X
Crystal Structure of P450BM3 mutant with N-perfluoroheptanoyl-L-tryptophan
- PDB DOI: https://doi.org/10.2210/pdb5B2X/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Priestia megaterium
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2016-02-03 Released: 2017-02-08
- Funding Organization(s): The Ministry of Education, Culture, Sports, Science, and Technology, The Japan Science and Technology Agency (JST)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.216
- R-Value Work: 0.180
- R-Value Observed: 0.181
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Bifunctional cytochrome P450/NADPH--P450 reductase | 456 | Priestia megaterium | Mutation(s): 1 Gene Names: cyp102A1, cyp102 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data) |  | |
UniProt | |||||
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779 Go to UniProtKB: P14779 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P14779 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEM Query on HEM | C [auth A], F [auth B] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L |  | ||
| W0T Query on W0T | D [auth A] | (2~{S})-3-(1~{H}-indol-3-yl)-2-[2,2,3,3,4,4,5,5,6,6,7,7,7-tridecakis(fluoranyl)heptanoylamino]propanoic acid C18 H11 F13 N2 O3 VIATWFKQWKXLPP-JTQLQIEISA-N |  | ||
| DMS Query on DMS | E [auth A], G [auth B] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.216
- R-Value Work: 0.180
- R-Value Observed: 0.181
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 58.402 | α = 90 |
| b = 147.355 | β = 100.1 |
| c = 64.301 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data collection |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-02-08 Deposition Author(s): Cong, Z., Shoji, O., Kasai, C., Sugimoto, H., Shiro, Y., Watanabe, Y.
| Funding Organization | Location | Grant Number |
|---|---|---|
| The Ministry of Education, Culture, Sports, Science, and Technology | Japan | 24225004 |
| The Ministry of Education, Culture, Sports, Science, and Technology | Japan | 15H05806 |
| The Japan Science and Technology Agency (JST) | Japan | 15658843 |
Revision History (Full details and data files)
- Version 1.0: 2017-02-08
Type: Initial release - Version 1.1: 2020-02-26
Changes: Data collection - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
